Genome-Wide Association Study of Waterlogging Tolerance in Barley (Hordeum vulgare L.) Under Controlled Field Conditions.

Ana Borrego-Benjumea,Meixue Zhou,Ana Badea,Min Zhu,James R Tucker,Adam Carter

doi:10.3389/fpls.2021.711654

Abstract

Waterlogging is one of the main abiotic stresses severely reducing barley grain yield. Barley breeding programs focusing on waterlogging tolerance require an understanding of genetic loci and alleles in the current germplasm. In this study, 247 worldwide spring barley genotypes grown under controlled field conditions were genotyped with 35,926 SNPs with minor allele frequency (MAF) > 0.05. Significant phenotypic variation in each trait, including biomass, spikes per plant, grains per plant, kernel weight per plant, plant height and chlorophyll content, was observed. A genome-wide association study (GWAS) based on linkage disequilibrium (LD) for waterlogging tolerance was conducted. Population structure analysis divided the population into three subgroups. A mixed linkage model using both population structure and kinship matrix (Q+K) was performed. We identified 17 genomic regions containing 51 significant waterlogging-tolerance-associated markers for waterlogging tolerance response, accounting for 5.8–11.5% of the phenotypic variation, with a majority of them localized on chromosomes 1H, 2H, 4H, and 5H. Six novel QTL were identified and eight potential candidate genes mediating responses to abiotic stresses were located at QTL associated with waterlogging tolerance. To our awareness, this is the first GWAS for waterlogging tolerance in a worldwide barley collection under controlled field conditions. The marker-trait associations could be used in the marker-assisted selection of waterlogging tolerance and will facilitate barley breeding.

Highlights

Waterlogging is a major abiotic stress that causes oxygen depletion and carbon oxide accumulation in the rhizosphere (Bailey-Serres and Voesenek, 2008) and has become one of the main concerns for crops limiting agricultural production globally
Six quantitative trait loci (QTL) (QPH.2H-1, QSP.1H-1, QSP.5H-1, QWLS.4H-1, QWLS.4H-2, and QWLS.6H) out of 20 were detected on genomic regions that have not been reported in previous waterlogging-related QTL studies on barley conducted using bi-parental populations and they probably represent novel loci for waterlogging tolerance
247 worldwide spring barley genotypes were evaluated for yield components-related traits under control and waterlogging treatment conditions in the field, as well as the relative difference between these two conditions, and were genotyped using Barley 50K iSelect single nucleotide polymorphism (SNP) Array

Summary

Introduction

Waterlogging is a major abiotic stress that causes oxygen depletion and carbon oxide accumulation in the rhizosphere (Bailey-Serres and Voesenek, 2008) and has become one of the main concerns for crops limiting agricultural production globally. Worldwide, 10–16% of the arable soils are affected by waterlogging (Setter and Waters, 2003; Yaduvanshi et al, 2014). In western Canada, waterlogging has been identified as an important limiting factor for the crops grown, including barley. Waterlogging causes an excess of ethylene and carbon dioxide that increases metabolic toxins and microelements such as iron and manganese in soil solution or roots, reduces respiration, root conductivity to water, and nutrient uptake, affecting plant growth and survival (Setter and Waters, 2003)

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